Evaluate gene sets identified by SDAN
Wei Sun
2024-07-04
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 2.00 21.00 22.00 20.98 22.00 23.00## [1] 40## [1] 2 18 19 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22 22 22
## [26] 22 22 22 22 22 22 22 22 22 23 23 23 23 23 23Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"##
## FALSE TRUE
## 1607 42##
## FALSE TRUE <NA>
## 42 1565 42gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: C10orf91 LINC02870
## 2: C12orf10 MYG1
## 3: C12orf45 NOPCHAP1
## 4: C6orf48 SNHG32
## 5: C6orf99 LINC02901
## 6: CXorf40A EOLA1
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM173A ANTKMT
## 10: FAM213B PRXL2B
## 11: H2AFX H2AX
## 12: HIST1H2AG H2AC11
## 13: HIST1H2BK H2BC12
## 14: HIST1H2BN H2BC15
## 15: HIST1H3A H3C1
## 16: HIST1H3H H3C10
## 17: HIST1H4C H4C3
## 18: HIST2H2BF H2BC18
## 19: KIAA0391 PRORP
## 20: QARS EPRS1
## 21: SEPT6 SEPTIN6
## 22: ARNTL BMAL1
## 23: C12orf65 MTRFR
## 24: C16orf72 HAPSTR1
## 25: CCDC84 CENATAC
## 26: DOPEY2 DOP1B
## 27: FAM126B HYCC2
## 28: FAM160B1 FHIP2A
## 29: H1FX H1-10
## 30: H2AFJ H2AJ
## 31: HEXDC HEXD
## 32: HIST1H1C H1-2
## 33: HIST1H1D H1-3
## 34: HIST1H1E H1-4
## 35: KIAA1109 BLTP1
## 36: KIAA1551 RESF1
## 37: MKL1 MRTFA
## 38: NARFL CIAO3
## 39: SEPT2 SEPTIN6
## 40: TARSL2 TARS3
## 41: TMEM8A PGAP6
## 42: WDR60 DYNC2I1
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1649 3## sym_in_data sym_limma gene_symbol
## 1: ABLIM1 ABLIM1 ABLIM1
## 2: AC004687.1 <NA> AC004687.1
## 3: AC004854.2 <NA> AC004854.2
## 4: AC007384.1 <NA> AC007384.1
## 5: AC007952.4 <NA> AC007952.4## t1
## 1 2
## 1647 1## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"## reactome go_bp immune
## 1692 7647 5219Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992Conduct enrichment analysis
## [1] 1649 3max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.1)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "CD83" "RHOC" "RPL41" "TLE4" "ASCL2" "CD226" "GNLY" "MKLN1"
## [9] "PLAC8" "PRR5L" "PTPN4" "SPN" "THADA" "TMSB10" "TMSB4X" "UVRAG"
## [17] "VPS18" "VPS39" "XPO6" "YPEL5" "ZZEF1"
## [1] 2
## [1] "DTHD1" "GSTM1" "NT5DC1" "SLC27A5" "SLC4A4" "TRAV8-4" "ZNF862"
## [8] "ADCY7" "ARAP2" "BICRAL" "DIAPH2" "DMTF1" "GPR141" "MCTP2"
## [15] "MIAT" "MTERF2" "MYBL1" "NFATC3" "NLRC3" "TUT7" "UNC13D"
## [22] "XIST" "ZNF83"
## [1] 3
## [1] "APMAP" "CD84" "CMC1" "FAM118A" "FCER1G" "ICAM3"
## [7] "KLRF1" "KLRG1" "LEPROTL1" "LETMD1" "LRRC23" "NCR1"
## [13] "RTN3" "SH2D1A" "THAP9-AS1" "TMEM107" "TMEM42" "MCOLN2"
## [19] "PATL2" "PCSK7" "RASA3" "SLFN5"
## [1] 4
## [1] "ARHGAP9" "CYB5D2" "HLA-DMB" "INTS8" "KLRB1" "MZT2A"
## [7] "PDE3B" "RCSD1" "ABCC1" "AHCTF1" "DOPEY2" "ENTPD4"
## [13] "HLA-DQA1" "KLRD1" "LPCAT1" "PNPLA6" "PTPN7" "SLC38A10"
## [19] "ST6GAL1" "TAP2" "UGGT1"
## [1] 5
## [1] "ACTR1B" "ATP5MG" "COQ7" "CPNE1" "FAM102A" "GLRX5"
## [7] "MARCKSL1" "MPST" "NMT2" "RACK1" "UIMC1" "WDR86"
## [13] "DNAJB14" "GDPD5" "HERC3" "HERC6" "KIAA0232" "NUP210"
## [19] "R3HCC1L" "ZNF335" "ZNF800"
## [1] 6
## [1] "AC245297.3" "AL139246.5" "BBS9" "CRTAM" "CXorf57"
## [6] "EOMES" "HIST1H3H" "MFNG" "NUAK2" "PITPNC1"
## [11] "TRAV12-2" "TRAV38-2DV8" "TRBV3-1" "TRBV6-2" "TRBV6-5"
## [16] "CYTOR" "FAM126B" "GK5" "GPR174" "NRDC"
## [21] "OGA" "PARP15" "PIK3R5"
## [1] 7
## [1] "NUCB2" "PAIP2" "PDLIM1" "PTGER4" "RPL22L1" "STMN3"
## [7] "CWC25" "DENND4C" "GIGYF1" "GPANK1" "HELZ" "KIF13B"
## [13] "L3HYPDH" "MAN2C1" "RNMT" "SCAF8" "SECISBP2" "TIMP1"
## [19] "ZCCHC2"
## [1] 8
## [1] "C10orf91" "ANKRD36B" "ANKRD36C" "C16orf72" "CD46" "CHD9"
## [7] "CROCC" "DGKD" "EML4" "MIGA1" "RNF19A" "RPS6KA5"
## [13] "RSAD2" "RUBCN" "STAT4" "STK10" "SYNE1" "UBE2H"
## [19] "UBR2" "VPS13C" "ZNF493" "ZNF708"
## [1] 9
## [1] "ALOX5AP" "HDHD3" "KLRK1" "MATK" "TMEM134" "ANKRD12" "BTBD9"
## [8] "CST7" "GZMA" "GZMB" "IRF9" "KLF3" "LILRB1" "MYO1F"
## [15] "NKG7" "RNF125" "SPON2" "SRGN" "TMEM181" "UCP2" "ZFAND3"
## [1] 10
## [1] "AC008555.5" "AC044849.1" "AC083798.2" "AL135791.1" "COQ8A"
## [6] "FAM213B" "HIKESHI" "MTRNR2L8" "NBPF14" "PCMTD2"
## [11] "PRAG1" "RGL4" "TOX" "TRAV13-1" "TRAV14DV4"
## [16] "TRAV5" "TRBV7-2" "TRBV7-9" "TRGV5" "TRGV7"
## [21] "WARS2" "ZNF749"
## [1] 12
## [1] "BTG1" "HIST1H4C" "ID2" "JADE1" "LDLRAP1" "MSC"
## [7] "PNRC1" "WDR54" "ZNF575" "ARRDC3" "BRPF1" "COX19"
## [13] "GCN1" "GON4L" "KAT6B" "MAPK8IP3" "PHF14" "PKD1"
## [19] "RORA" "USP16" "ZNF292"
## [1] 13
## [1] "AC004687.1" "AC004854.2" "AC015982.1" "AC020911.2" "AC083880.1"
## [6] "AC091271.1" "AC103591.3" "AF213884.3" "AL357060.1" "AL451085.1"
## [11] "AL627171.1" "ARF4-AS1" "ATP2B1-AS1" "C6orf99" "HELQ"
## [16] "HIPK1-AS1" "KCNQ1OT1" "LINC01465" "MZF1-AS1" "OSER1-DT"
## [21] "PGGHG" "NEK9"
## [1] 14
## [1] "AOAH" "CCL4L2" "TRAV3" "TRG-AS1" "TRGV8" "TRGV9"
## [7] "CARD11" "CARD16" "EPSTI1" "FCRL6" "FGL2" "ITM2A"
## [13] "LINC02384" "NECAP1" "PTPRJ" "TRAV9-2" "TRDC" "TRDV1"
## [19] "TRGC2" "TRGV4" "TTC38" "XCL2"
## [1] 15
## [1] "ASAH1" "COMMD6" "COTL1" "ITGB1BP1" "LAPTM5" "NSUN6"
## [7] "PTPRCAP" "TPGS2" "CCNH" "CD2" "CD52" "CD8A"
## [13] "CD8B" "ITK" "LY6E" "PRSS23" "RHOH" "SBK1"
## [19] "SLC35F5" "TRAC" "TRBC2" "ZDHHC20"
## [1] 16
## [1] "TPRKB" "BDP1" "CHD1" "DHX29" "HELZ2" "HEXDC" "IFI44"
## [8] "IFIT2" "IFIT3" "KLHDC4" "MSI2" "MX1" "NEMF" "OAS3"
## [15] "PHACTR4" "PLA2G6" "REXO1" "RNF157" "RNPC3" "SPOCK2" "VAV3"
## [22] "ZC3H7B"
## [1] 17
## [1] "IL6R" "SERINC5" "TRBV6-1" "ABCA5" "ABR"
## [6] "AC020659.1" "CCDC84" "CPPED1" "DDX3Y" "EIF1AY"
## [11] "ENOSF1" "IL6ST" "KDM5D" "MICAL2" "OSM"
## [16] "RPS4Y1" "SBNO2" "SIDT1" "TRBV4-2" "ZMIZ2"
## [21] "ZNF236" "ZNF652"
## [1] 18
## [1] "ARHGAP45" "CEMIP2" "CRYBG1" "FAM133B" "MX2"
## [6] "OAS2" "PIK3CD" "PPP4R3B" "PREX1" "PUM3"
## [11] "RIPOR2" "S100A12" "SAMD9L" "TENT5C" "THUMPD3-AS1"
## [16] "TMEM131L" "TRANK1" "TRAV19" "TRAV27" "TRBV11-2"
## [21] "TRBV2" "TUT4"
## [1] 19
## [1] "AMD1" "CD27" "CREBL2" "CYB561A3" "EI24" "GIMAP1"
## [7] "GLTP" "IER3" "IFRD1" "KIR3DL2" "LIME1" "MZF1"
## [13] "NELL2" "PDE7A" "PPP1R15B" "SLC38A1" "TMEM204" "TSPYL4"
## [19] "LTBP4" "TRIM38" "VPS13A" "ZBTB40"
## [1] 20
## [1] "RGCC" "ACOX1" "BTN3A1" "CAST" "CCDC88C" "CELF2"
## [7] "DDHD1" "KDM5A" "MTMR6" "NCKAP1L" "NLRC5" "PCYT1A"
## [13] "PRKCH" "RAP1GAP2" "RASGRP1" "SPG11" "SYNRG" "TAOK1"
## [19] "TAOK3" "TIPARP" "ZEB2"
## [1] 21
## [1] "ID1" "RGS1" "AC092683.1" "AP005482.1" "ATAD2B"
## [6] "BMT2" "DOCK10" "ETFDH" "FAM78A" "GABPB2"
## [11] "GRK2" "HRH2" "IGKV3-15" "LINC02256" "MARF1"
## [16] "MINDY2" "NBEAL2" "POLR2J3-1" "SEC14L1" "THAP5"
## [21] "Z93930.2" "ZNF808"
## [1] 22
## [1] "ARL4A" "ABCA7" "CAPNS1" "ELMO1" "ERICH1" "FAM53B"
## [7] "FNBP1" "HSH2D" "IFI44L" "IL2RG" "IRAK4" "KCNAB2"
## [13] "KIAA1551" "KIAA2026" "KLF6" "PNPLA8" "PRDM2" "SENP7"
## [19] "TTC14" "WASL" "XAF1"
## [1] 23
## [1] "AC012645.3" "AC027644.3" "AC087623.3" "AK5" "AL118516.1"
## [6] "BX284668.6" "CHRM3-AS2" "FXYD7" "IGLV1-44" "INTS6L"
## [11] "KMT2E-AS1" "LINC00402" "LINC00649" "LST1" "MAP3K2"
## [16] "MATR3-1" "PDCD4-AS1" "RETREG1" "SNHG15" "TRAV21"
## [21] "TRAV8-2" "TRAV8-3"
## [1] 24
## [1] "C12orf45" "CAMK4" "CRLF3" "GCH1" "PLK2" "ZNF10"
## [7] "ANKRD44" "EHMT1" "FRYL" "MBD5" "PIGF" "POLH"
## [13] "PPP6R2" "PRR14L" "RLF" "SETD2" "SETX" "SP3"
## [19] "USP34" "WDR7" "ZNF407"
## [1] 25
## [1] "AL136454.1" "ATP5F1A" "CCNI" "COA1" "EFCAB2"
## [6] "FAM173A" "FCMR" "FCRL3" "GCSAM" "GTF3A"
## [11] "ITGAE" "RTRAF" "TRBC1" "ADGRE5" "ARHGAP30"
## [16] "CD38" "CTSW" "IFITM2" "MT2A" "MYO1G"
## [21] "SLA2" "ZNF683"
## [1] 26
## [1] "AIF1" "CD28" "YPEL3" "ANKRD49" "CASP10" "CFLAR"
## [7] "ETNK1" "FNDC3B" "GCA" "GPATCH2L" "H6PD" "IGHA1"
## [13] "LSS" "NCOA7" "PHF11" "PRKX" "PTGDS" "SETD5"
## [19] "WDTC1"
## [1] 27
## [1] "GNAQ" "NXT2" "AC016831.7" "ADHFE1" "AKNA"
## [6] "APOL6" "ARL4C" "ELMOD3" "GBP1" "GBP5"
## [11] "GNPTAB" "GPR132" "IFI27" "INPP4A" "ISG20"
## [16] "PDZD4" "PPP1R16B" "RAB27B" "SLFN12L" "SYTL3"
## [21] "TTC16"
## [1] 28
## [1] "BTG2" "C12orf10" "C12orf57" "CCNL1" "GSTM4" "KCTD7"
## [7] "MAP3K8" "MAPRE2" "NELFCD" "NEU1" "PTRHD1" "RPS26"
## [13] "RSRP1" "SEPT6" "SMDT1" "TGIF1" "ZFP36L1" "ACAP3"
## [19] "PARP4" "TEP1"
## [1] 29
## [1] "AC016405.3" "AC087239.1" "AC245014.3" "ANXA2R" "CITED2"
## [6] "CSKMT" "CXorf40A" "IER5" "IGKV3-20" "ILF3-DT"
## [11] "NOCT" "PIK3IP1" "SDR42E2" "SLC2A3" "SLC38A2"
## [16] "STK17A" "TC2N" "TRBV28" "WSB1" "Z93241.1"
## [21] "ZFAS1" "MALAT1"
## [1] 30
## [1] "BACH2" "CSRNP1" "EGR1" "EPS8" "FOSB" "MYLIP" "NOSIP" "NR1D1"
## [9] "NR4A2" "NR4A3" "RCAN3" "SELL" "SNHG12" "TCF7" "TXK" "CYTH1"
## [17] "DUS1L" "JUND" "MIDN" "SCRN3" "VCAN"
## [1] 31
## [1] "ASL" "CLDND1" "CXXC5" "GATA3" "PAPSS1" "RAB33B" "SESN1"
## [8] "SESN2" "TBCCD1" "TIGIT" "CSNK1G2" "ERAP2" "GALNT3" "ITGAM"
## [15] "KIR2DL3" "PYROXD1" "RAPGEF1" "RUFY2" "SZT2" "TBX21" "VPS13B"
## [22] "YPEL1" "ZDHHC5"
## [1] 32
## [1] "NT5E" "TBC1D17" "AFF1" "AFF4" "ARHGAP4" "BAZ2A" "CEP164"
## [8] "CRNKL1" "LRRFIP1" "LUC7L3" "NKTR" "PNN" "PPIG" "PPIL2"
## [15] "SRSF10" "SRSF11" "WDR60" "YTHDC1"
## [1] 33
## [1] "ZC3H12A" "B4GALT1" "BCL9L" "C2CD3" "CAPN15" "EHBP1L1" "LONP2"
## [8] "LPIN1" "NAA25" "NFKBIZ" "PDE4B" "PDE4D" "PIM1" "RALGAPB"
## [15] "RIC3" "STK17B" "TBC1D2B" "TOB1" "UTY" "ZBTB20"
## [1] 34
## [1] "GALNT11" "ADGRG1" "ARHGAP10" "CCL4" "CES1" "CX3CR1"
## [7] "ERBIN" "FGFBP2" "GALNT10" "GALNT2" "ITGAL" "LAG3"
## [13] "MPPE1" "MYO9B" "PEX1" "PEX26" "PLEK" "SEMA4D"
## [19] "ST8SIA4" "SUSD1" "TMEM8A"
## [1] 35
## [1] "HMBOX1" "KIF9" "ANKRD36" "AP3B1" "AP3M2" "ARAP1" "ARID5B"
## [8] "ATG2A" "ATG2B" "CLEC16A" "CREBZF" "FAM13B" "GPRIN3" "HECTD4"
## [15] "INO80" "INO80D" "INPP5D" "KLF2" "MKL1" "NARFL" "NFE2L1"
## [22] "PIP4K2B" "ZNF557"
## [1] 36
## [1] "AC025164.1" "AL121944.1" "AL138963.3" "ARMH1" "C6orf48"
## [6] "CCR7" "INPP4B" "JAML" "LINC02273" "LRRN3"
## [11] "LTB" "NPIPB4" "NUP58" "TCEA3" "TMIGD2"
## [16] "TNFRSF25" "TRABD2A" "TRAV1-2" "TRBV9" "OXNAD1"
## [21] "PARP11" "PCED1B"
## [1] 37
## [1] "AC007952.4" "AC119396.1" "ALKBH7" "BNIP3L" "CD40LG"
## [6] "CMTM7" "DYRK4" "EPB41L4A-AS1" "EPHX2" "GADD45B"
## [11] "GZMK" "HIBADH" "MCUB" "NOP53" "RGS10"
## [16] "SNHG8" "TCP11L2" "TESPA1" "TRBV20-1" "ZFAND1"
## [21] "ITPR2" "LINC02446"
## [1] 38
## [1] "CST3" "MAN2B1" "SAE1" "TRAT1" "ATP2B4" "CCDC112"
## [7] "CMKLR1" "CTSC" "DOCK11" "FAM169A" "LNPEP" "LRRC8A"
## [13] "PARP14" "RAB3GAP2" "SLC4A7" "SLK" "TMEM127" "TTC17"
## [19] "VPS13D" "ZNF276"
## [1] 39
## [1] "ABCC10" "ARHGEF3" "COL6A2" "COL6A3" "DDX60L"
## [6] "DENND4B" "EIF4E3" "HECA" "HPS4" "LAIR2"
## [11] "N4BP1" "NUTM2B-AS1" "ODF3B" "SUSD6" "TRAV12-3"
## [16] "TRAV17" "TRAV4" "TRBV7-6" "TRGV10" "TSPAN32"
## [21] "TTTY15" "XCL1" "ZBP1"
## [1] 40
## [1] "AC007384.1" "AC025171.3" "ARRDC2" "NT5C3B" "PRR7"
## [6] "SNHG9" "AC116407.2" "ARHGEF9" "BROX" "CHD6"
## [11] "DDIT4" "GPHN" "HIPK1" "IQCG" "KIAA1109"
## [16] "PCNX1" "PSMA3-AS1" "SLC16A1-AS1" "SLCO3A1" "SLF2"
## [21] "SPATA13" "TARSL2" "VTI1A"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_1"
## [1] "CD83" "RHOC" "RPL41" "TLE4" "ASCL2" "CD226" "GNLY" "MKLN1"
## [9] "PLAC8" "PRR5L" "PTPN4" "SPN" "THADA" "TMSB10" "TMSB4X" "UVRAG"
## [17] "VPS18" "VPS39" "XPO6" "YPEL5" "ZZEF1"
## $reactome
## category over_represented_pvalue
## 895 sars cov 2 modulates autophagy 2.230272e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 895 1 3 3 0.002593807
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 4354 snare complex assembly 2.79997e-06 1
## numDEInCat numInCat FDR
## 4354 3 3 0.01313466
##
## [1] "set_3"
## [1] "APMAP" "CD84" "CMC1" "FAM118A" "FCER1G" "ICAM3"
## [7] "KLRF1" "KLRG1" "LEPROTL1" "LETMD1" "LRRC23" "NCR1"
## [13] "RTN3" "SH2D1A" "THAP9-AS1" "TMEM107" "TMEM42" "MCOLN2"
## [19] "PATL2" "PCSK7" "RASA3" "SLFN5"
## $reactome
## category
## 435 immunoregulatory interactions between a lymphoid and a non lymphoid cell
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 435 8.235374e-06 0.9999998 5 34
## FDR
## 435 0.00957774
##
## [1] "set_9"
## [1] "ALOX5AP" "HDHD3" "KLRK1" "MATK" "TMEM134" "ANKRD12" "BTBD9"
## [8] "CST7" "GZMA" "GZMB" "IRF9" "KLF3" "LILRB1" "MYO1F"
## [15] "NKG7" "RNF125" "SPON2" "SRGN" "TMEM181" "UCP2" "ZFAND3"
## $immune
## category
## 4250 gse45739 unstim vs acd3 acd28 stim nras ko cd4 tcell dn
## 4981 kazmin pbmc p falciparum rtss as01 age unknown correlated with protection 56dy ne
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4250 3.623625e-06 0.9999998 7 54
## 4981 6.626185e-06 0.9999998 5 22
## FDR
## 4250 0.01689015
## 4981 0.01689015
##
## [1] "set_15"
## [1] "ASAH1" "COMMD6" "COTL1" "ITGB1BP1" "LAPTM5" "NSUN6"
## [7] "PTPRCAP" "TPGS2" "CCNH" "CD2" "CD52" "CD8A"
## [13] "CD8B" "ITK" "LY6E" "PRSS23" "RHOH" "SBK1"
## [19] "SLC35F5" "TRAC" "TRBC2" "ZDHHC20"
## $go_bp
## category over_represented_pvalue
## 4477 t cell receptor signaling pathway 1.445094e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4477 0.9999993 6 43 0.06778935
##
## [1] "set_16"
## [1] "TPRKB" "BDP1" "CHD1" "DHX29" "HELZ2" "HEXDC" "IFI44"
## [8] "IFIT2" "IFIT3" "KLHDC4" "MSI2" "MX1" "NEMF" "OAS3"
## [15] "PHACTR4" "PLA2G6" "REXO1" "RNF157" "RNPC3" "SPOCK2" "VAV3"
## [22] "ZC3H7B"
## $immune
## category
## 1342 gse18791 unstim vs newcatsle virus dc 10h dn
## 5074 sobolev pbmc pandemrix age 18 64yo 7dy dn
## 1368 gse18893 tconv vs treg 24h culture dn
## 4081 gse42724 naive bcell vs plasmablast up
## 1338 gse18791 ctrl vs newcastle virus dc 6h dn
## 5055 querec pbmc yf 17d vaccine age 18 45yo 3dy up
## 5056 querec pbmc yf 17d vaccine age 18 45yo 7dy up
## 1453 gse19888 adenosine a3r inh vs act with inhibitor pretreatment in mast cell up
## 10 erwin cohen blood tc 83 age 23 48yo vaccinated vs control 2dy up
## 4874 gse9960 gram neg vs gram neg and pos sepsis pbmc up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1342 3.851459e-07 1.0000000 8 55
## 5074 7.535735e-07 1.0000000 5 14
## 1368 3.311437e-06 0.9999999 6 34
## 4081 6.338755e-06 0.9999996 7 55
## 1338 1.595504e-05 0.9999989 7 63
## 5055 1.606477e-05 0.9999994 5 24
## 5056 1.606477e-05 0.9999994 5 24
## 1453 2.393285e-05 0.9999986 6 44
## 10 2.771849e-05 0.9999983 6 45
## 4874 3.128033e-05 0.9999986 5 28
## FDR
## 1342 0.001920859
## 5074 0.001920859
## 1368 0.005627235
## 4081 0.008078743
## 1338 0.011699744
## 5055 0.011699744
## 5056 0.011699744
## 1453 0.015251207
## 10 0.015700984
## 4874 0.015946710
##
## [1] "set_17"
## [1] "IL6R" "SERINC5" "TRBV6-1" "ABCA5" "ABR"
## [6] "AC020659.1" "CCDC84" "CPPED1" "DDX3Y" "EIF1AY"
## [11] "ENOSF1" "IL6ST" "KDM5D" "MICAL2" "OSM"
## [16] "RPS4Y1" "SBNO2" "SIDT1" "TRBV4-2" "ZMIZ2"
## [21] "ZNF236" "ZNF652"
## $reactome
## category over_represented_pvalue
## 478 interleukin 6 family signaling 2.671849e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 478 0.9999998 3 8 0.03107361
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 4122 response to interleukin 6 1.242271e-05 0.9999999
## numDEInCat numInCat FDR
## 4122 3 5 0.05827493
##
## [1] "set_18"
## [1] "ARHGAP45" "CEMIP2" "CRYBG1" "FAM133B" "MX2"
## [6] "OAS2" "PIK3CD" "PPP4R3B" "PREX1" "PUM3"
## [11] "RIPOR2" "S100A12" "SAMD9L" "TENT5C" "THUMPD3-AS1"
## [16] "TMEM131L" "TRANK1" "TRAV19" "TRAV27" "TRBV11-2"
## [21] "TRBV2" "TUT4"
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 2154 neutrophil chemotaxis 1.564504e-05 0.9999997
## 2160 neutrophil migration 2.912363e-05 0.9999993
## 1047 granulocyte chemotaxis 3.103883e-05 0.9999992
## 1050 granulocyte migration 5.931136e-05 0.9999983
## numDEInCat numInCat FDR
## 2154 4 19 0.04853439
## 2160 4 22 0.04853439
## 1047 4 22 0.04853439
## 1050 4 26 0.06955740
##
## [1] "set_19"
## [1] "AMD1" "CD27" "CREBL2" "CYB561A3" "EI24" "GIMAP1"
## [7] "GLTP" "IER3" "IFRD1" "KIR3DL2" "LIME1" "MZF1"
## [13] "NELL2" "PDE7A" "PPP1R15B" "SLC38A1" "TMEM204" "TSPYL4"
## [19] "LTBP4" "TRIM38" "VPS13A" "ZBTB40"
## $immune
## category over_represented_pvalue
## 1977 gse22886 naive tcell vs monocyte up 1.476627e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1977 0.9999989 7 64 0.07527844
##
## [1] "set_30"
## [1] "BACH2" "CSRNP1" "EGR1" "EPS8" "FOSB" "MYLIP" "NOSIP" "NR1D1"
## [9] "NR4A2" "NR4A3" "RCAN3" "SELL" "SNHG12" "TCF7" "TXK" "CYTH1"
## [17] "DUS1L" "JUND" "MIDN" "SCRN3" "VCAN"
## $reactome
## category over_represented_pvalue
## 645 nuclear receptor transcription pathway 5.987482e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 645 0.9999994 3 6 0.06963441
##
## $immune
## category
## 4345 gse4984 lps vs vehicle ctrl treated dc up
## 3878 gse40666 stat1 ko vs stat4 ko cd8 tcell with ifna stim 90min dn
## 708 gse15733 bm vs spleen memory cd4 tcell dn
## 3537 gse37605 foxp3 fusion gfp vs ires gfp treg c57bl6 up
## 5021 nakaya pbmc fluarix fluvirin age 18 50yo 7dy dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4345 8.073533e-06 0.9999997 5 26
## 3878 3.607021e-05 0.9999984 5 26
## 708 5.836425e-05 0.9999970 5 33
## 3537 5.870079e-05 0.9999971 5 28
## 5021 8.787659e-05 0.9999917 7 76
## FDR
## 4345 0.04115887
## 3878 0.07481416
## 708 0.07481416
## 3537 0.07481416
## 5021 0.08959897
##
## [1] "set_31"
## [1] "ASL" "CLDND1" "CXXC5" "GATA3" "PAPSS1" "RAB33B" "SESN1"
## [8] "SESN2" "TBCCD1" "TIGIT" "CSNK1G2" "ERAP2" "GALNT3" "ITGAM"
## [15] "KIR2DL3" "PYROXD1" "RAPGEF1" "RUFY2" "SZT2" "TBX21" "VPS13B"
## [22] "YPEL1" "ZDHHC5"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 47 amino acids regulate mtorc1 4.312411e-05 0.9999996
## numDEInCat numInCat FDR
## 47 3 6 0.05015334
##
## [1] "set_32"
## [1] "NT5E" "TBC1D17" "AFF1" "AFF4" "ARHGAP4" "BAZ2A" "CEP164"
## [8] "CRNKL1" "LRRFIP1" "LUC7L3" "NKTR" "PNN" "PPIG" "PPIL2"
## [15] "SRSF10" "SRSF11" "WDR60" "YTHDC1"
## $reactome
## category over_represented_pvalue
## 579 mrna splicing 2.449222e-07
## 721 processing of capped intron containing pre mrna 8.173826e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 579 1 7 38 0.0002848445
## 721 1 7 45 0.0004753080
##
## $go_bp
## category over_represented_pvalue
## 4255 rna splicing 3.815935e-07
## 4395 spliceosomal complex assembly 1.192757e-05
## 1584 mrna splice site recognition 7.284369e-05
## 4257 rna splicing via transesterification reactions 8.480068e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4255 1.0000000 8 72 0.001790055
## 4395 0.9999998 4 14 0.027976117
## 1584 0.9999991 3 8 0.099449994
## 4257 0.9999955 5 43 0.099449994
##
## [1] "set_34"
## [1] "GALNT11" "ADGRG1" "ARHGAP10" "CCL4" "CES1" "CX3CR1"
## [7] "ERBIN" "FGFBP2" "GALNT10" "GALNT2" "ITGAL" "LAG3"
## [13] "MPPE1" "MYO9B" "PEX1" "PEX26" "PLEK" "SEMA4D"
## [19] "ST8SIA4" "SUSD1" "TMEM8A"
## $reactome
## category over_represented_pvalue
## 654 o linked glycosylation of mucins 3.406216e-05
## 653 o linked glycosylation 6.745152e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 654 0.9999998 3 5 0.03922306
## 653 0.9999993 3 6 0.03922306
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 2230 o glycan processing 1.881402e-05 0.9999999
## 1031 glycosylation 1.935866e-05 0.9999996
## numDEInCat numInCat FDR
## 2230 3 5 0.04540574
## 1031 4 14 0.04540574
##
## $immune
## category over_represented_pvalue
## 4252 gse45739 unstim vs acd3 acd28 stim wt cd4 tcell dn 1.901911e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4252 0.9999986 7 70 0.09695942
##
## [1] "set_36"
## [1] "AC025164.1" "AL121944.1" "AL138963.3" "ARMH1" "C6orf48"
## [6] "CCR7" "INPP4B" "JAML" "LINC02273" "LRRN3"
## [11] "LTB" "NPIPB4" "NUP58" "TCEA3" "TMIGD2"
## [16] "TNFRSF25" "TRABD2A" "TRAV1-2" "TRBV9" "OXNAD1"
## [21] "PARP11" "PCED1B"
## $immune
## category over_represented_pvalue
## 2391 gse26495 naive vs pd1high cd8 tcell up 4.581605e-06
## 2393 gse26495 naive vs pd1low cd8 tcell up 8.116493e-06
## 142 gse11057 naive vs cent memory cd4 tcell up 5.570191e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2391 0.9999999 5 30 0.02068894
## 2393 0.9999998 5 33 0.02068894
## 142 0.9999984 4 25 0.09465612
##
## [1] "set_39"
## [1] "ABCC10" "ARHGEF3" "COL6A2" "COL6A3" "DDX60L"
## [6] "DENND4B" "EIF4E3" "HECA" "HPS4" "LAIR2"
## [11] "N4BP1" "NUTM2B-AS1" "ODF3B" "SUSD6" "TRAV12-3"
## [16] "TRAV17" "TRAV4" "TRBV7-6" "TRGV10" "TSPAN32"
## [21] "TTTY15" "XCL1" "ZBP1"
## $reactome
## category
## 159 collagen biosynthesis and modifying enzymes
## 160 collagen chain trimerization
## 72 assembly of collagen fibrils and other multimeric structures
## 162 collagen formation
## 590 ncam1 interactions
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 159 9.184822e-05 1.0000000 2 2
## 160 9.184822e-05 1.0000000 2 2
## 72 2.146121e-04 0.9999995 2 3
## 162 2.146121e-04 0.9999995 2 3
## 590 2.835424e-04 0.9999992 2 3
## FDR
## 159 0.05340974
## 160 0.05340974
## 72 0.06239846
## 162 0.06239846
## 590 0.06595195Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958444 478.5 16391124 875.4 NA 16391124 875.4
## Vcells 19169726 146.3 73326430 559.5 65536 91658037 699.3## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1